We use the R package pointblank
to review and validate the plot-level descriptors
(HDP_plots.csv) and clean demographic data set
(heliconia_data_clean.csv) in preparation for archiving in
Dryad and publication in Bruna et al. (2023). The report below
includes:
Tests to determine if columns are correctly coded as integer,
character, etc.
Test criteria: Strict (‘stop’ if any rows
fail).
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Height is measured to nearest cm
|
— |
|
✓ |
57K |
57K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 2 | Shoots is interger
|
— |
|
✓ |
57K |
57K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 3 | Number of inflorescences is integer
|
— |
|
✓ |
2K |
2K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 2023-05-26 18:03:35 EDT < 1 s 2023-05-26 18:03:35 EDT | |||||||||||||
Test for any nonexistent values of plot_id (e.g.,
‘FF-10’, ‘CF-23’) or subplot (e.g., ‘H23’, ‘A11’).
Test criteria: Strict (‘stop’ if any rows
fail).
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | col_vals_in_set()
|
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | |||
| 2 | col_vals_in_set()
|
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | |||
| 2023-05-26 18:03:36 EDT < 1 s 2023-05-26 18:03:37 EDT | |||||||||||||
Tests for duplicated rows, missing plant_ID numbers, or
duplicate plant_id numbers (test is done for every survey
year).
Test criteria: Strict (‘stop’ if any rows
fail).
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | duplicated rows
|
— | — |
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | |
| 2 | col_vals_not_null()
|
— |
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 3 | Check for duplicate plant ID numbers
|
— |
|
✓ |
9K |
9K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 4 | Check for duplicate tag numbers in a plot
|
— |
|
✓ |
64 |
00.00 |
641.00 |
— |
● |
— |
|||
| 2023-05-26 18:03:38 EDT 4.2 s 2023-05-26 18:03:42 EDT | |||||||||||||
Tests to determine how many values of plant size (shts,
ht) or infloresence number (infl) are outside
the range of most values.
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if
\(\geq\) 2% of rows fail
conditions.
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | shoots between 0 and 20
|
|
✓ |
67K |
67K0.99 |
80.01 |
● |
○ |
— |
||||
| 2 | height between 0 and 200cm
|
|
✓ |
67K |
67K0.99 |
20.01 |
● |
○ |
— |
||||
| 3 | infloresences between 0 and 3
|
|
✓ |
67K |
67K0.99 |
150.01 |
● |
○ |
— |
||||
| 2023-05-26 18:03:43 EDT < 1 s 2023-05-26 18:03:43 EDT | |||||||||||||
Tests for unusual changes in plant size (both height and shoot
number) from \(Year_{t}\) to \(Year_{t+1}\).
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if
\(\geq\) 2% of rows fail
conditions.
| Pointblank Validation | |||||||||||||
| Check growth & regression
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |% change in height| < 200%
|
|
✓ |
67K |
66K0.99 |
4200.01 |
● |
○ |
— |
||||
| 2 | |∆ height| < 100cm
|
|
✓ |
67K |
67K0.99 |
110.01 |
— |
● |
— |
||||
| 3 | |∆ shoot number| < 5
|
|
✓ |
67K |
67K0.99 |
2010.01 |
— |
● |
— |
||||
| 2023-05-26 18:03:44 EDT < 1 s 2023-05-26 18:03:44 EDT | |||||||||||||
Tests for seedlings whose size at initial marking was unusually
large. Conducted for both height and shoot number.
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if
\(\geq\) 2% of rows fail
conditions.
| Pointblank Validation | |||||||||||||
| Check seedlings
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | shoots < 3
|
|
✓ |
3K |
3K0.99 |
120.01 |
● |
○ |
— |
||||
| 2 | height < 30cm
|
|
✓ |
3K |
3K0.99 |
30.01 |
● |
○ |
— |
||||
| 2023-05-26 18:03:45 EDT < 1 s 2023-05-26 18:03:45 EDT | |||||||||||||
Graphical depiction of the proportion of plants in each demographic plot for which there is no measurement of plant height (e.g., if plant not found).